Variant report

Variant	rs7544656
Chromosome Location	chr1:222009827-222009828
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:221913929..221915461-chr1:222008907..222010428,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143507	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11577677	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11590053	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17010889	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3010850	0.85[EUR][1000 genomes]
rs4418610	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4528124	0.82[JPT][hapmap]
rs4551601	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4639769	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61825191	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61825193	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61825195	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7514382	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7515604	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7519761	0.82[JPT][hapmap]
rs9441877	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9441974	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9441979	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469786	chr1:221855871-222040335	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv482867	chr1:221855871-222040335	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1002463	chr1:221863355-222095773	Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv535302	chr1:221863355-222095773	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:222000000-222010200	Enhancers	HMEC	breast
2	chr1:222000600-222019000	Weak transcription	Lung	lung
3	chr1:222000800-222011000	Weak transcription	Thymus	Thymus
4	chr1:222001200-222011000	Weak transcription	Fetal Thymus	thymus
5	chr1:222004200-222011000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr1:222004200-222012800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr1:222004400-222011000	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr1:222004600-222011200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr1:222005800-222019000	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr1:222006200-222012600	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr1:222006400-222011400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr1:222006800-222012600	Weak transcription	Esophagus	oesophagus
13	chr1:222007000-222010600	Enhancers	Hela-S3	cervix
14	chr1:222007600-222011400	Weak transcription	HUVEC	blood vessel
15	chr1:222007800-222010000	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr1:222008200-222013400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr1:222008400-222012600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr1:222008600-222012600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr1:222008600-222012600	Weak transcription	NHEK	skin
20	chr1:222008800-222013800	Weak transcription	Fetal Lung	lung
21	chr1:222008800-222018800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr1:222009000-222012800	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr1:222009200-222011000	Enhancers	GM12878-XiMat	blood
24	chr1:222009400-222010000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr1:222009400-222010800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr1:222009400-222012600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr1:222009400-222012800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr1:222009600-222012800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr1:222009600-222013200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr1:222009800-222010000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr1:222009800-222010000	Enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr1:222009800-222011200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr1:222009800-222012600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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